Been there done that!
Best thing to do is pull the vent off and lightly sand the edge smooth almost to the point of polishing the bottom edge and out side edge smooth.
Then before you reattach it to the lid .. lightly push down on the center of the vent to flatten it out just a little bit. I placed the vent on 2-3 layers of shop towels on a hard FLAT surface and using the heat of my hand gently push it to form it flatter to match the lid.
NOT totally flat! By looking at the air gap around the 4 air holes you will know when it is sitting better.
Doing this will make your air control way easier and also help when you shut the grill down!
And do not tighten the snot out of the bolt!! You have to play with it to get the correct feel!
Now is the time to replace the nut and bolt with SS hardware and SS washers!
Hope this helps.
I just received a new JJ and this was a very helpful comment to read before assembling it. I rounded the inside edges of both vents, sanded them up to 800 grit, and very carefully tightened the screws until the vents were secure but free to move. They feel nice and smooth and I'm much less worried about scratches now.
Do you have any tips for avoiding chips where the lid bail washers are pressed against the bottom bowl? It seems like it's been a common issue for the JJ since day one.
